Alterante Reality: The Trials of Emerald
by tkdgoddess44
Summary: In an alternate reality of the pokemon universe a girl named Emerald must face many hardships and learn many truths if she hopes to survive.
1. Prologue

Disclaimer: I do not in any way shape or form own anything pokemon related. Emerald is mine though.

Alternate Reality: A Trainer Named Emerald

Prologue:

Chaos...There were men laughing everywhere. Emerald didn't know where to go or what to do. Where was her family...her father...her mother...her baby brother? She didn't know where any of them were. She couldn't stay here for long; they would find her. She suddenly coughed and smelled smoke. Where they burning her house as well? What had her family done?

"Search the room, we still haven't found the daughter." "Yes Sir!" She heard footsteps and furniture being overturned. The sounds were coming closer and she held her breath. She leaned back against the cabinet she was hiding in as far as she could and placed her teddy in front of her. One of the doors opened and she saw the shadow of a hand reach inside. Panic rose inside of her as she pressed her head harder and harder against the wall even though she couldn't go back any farther.

The hand began reaching straight towards her and she closed her eyes. When nothing happened she opened them again and saw that he was almost touching her cheek. She looked up and saw two young ice-blue eyes stare directly into her own. He knew she was in here; what were they going to do to her.

Suddenly he reached down and grabbed her teddy pulling it out with more force than was necessary. "Huh, just a bear; the room's all clear boss." "Okay, let's keep looking." Emerald heard his retreating footsteps and peaked out from a crack in the opening of the cabinet. She saw a blood-red letter on the front of his black uniform and leaned back.

When she was sure that they were gone she climbed out of the cabinet and raced towards the window. It was night out and raining heavily. She opened the window and jumped out landing lightly on her feet. She landed in a mud puddle and her stockings were soaked. She fearfully looked around for any of the bad men.

She heard voices from around the corner and quickly ran towards the woods. She tripped over something and quickly scrambled back up. She looked back and felt panic rise within her. It was her nanny, she was lying face down and there was red all over her. She backed away and started to run into the woods as fast as she could. She didn't stop for a long time for fear that they would get her. Her dress was torn everywhere and her stockings were in shreds.

She exited the forest and found herself at the beach. Her home was located in the middle of an island. She collapsed on the sand and began to notice how her entire body was sore from running. She would have stayed there if she hadn't noticed a blinking red light near the water. She slowly picked herself up and walked over to it. As she got closer she noticed that there were two blinking lights. There was a Starmie and a Staryu. She went to her knees in front of the Starmie and she almost let out a shriek of horror.

Its body was mutilated; she was surprised that it was still alive. There were cuts all over where a silver substance she could only assume was blood was coming through. She ripped off part of her dress and began to frantically try to stop the pokemon from bleeding. She stopped when she saw the crystal in the middle of its body; parts of it were missing and the rest was cracked. Her hands began shaking and tears fell down her cheeks; this pokemon was going to die and there was nothing she could do about it. The rain continued to fall on her as she tried to contain her sobs.

Her family was most likely captured or dead. After all, those men had said that they were still looking for the daughter. They didn't say they were looking for anyone else. This poor Starmie was dying; it looked like it had been in a fierce battle and she was all alone. She didn't know anyone besides those that had worked in her house. She had never been allowed to go off of the island.

She gently laid her hand on the crystal. "I'm sorry...." Suddenly she heard a voice whispering in the back of her mind. '_not me...save child..._' "What?" She looked at the Starmie, and then she saw the Staryu several feet away. It was inching its way towards the Starmie. She got up and went over to it. It had a deep wound on one of its arms and that's why it was moving so slow. She picked it up; it was hardly larger than her hand. It was just a baby...wait...it was the Starmie's baby. The Staryu began a weak struggle but she placed it next to its parent and it stopped. '_thank you...take care...child...please...'_

Tears began fall freely down her face as she touched the shattered crystal once more. "I will..." She felt a spark race up her spine and the crystal finally stopped blinking. She couldn't contain herself anymore and finally heart-wrenching sobs escaped from her battered body.

She felt a cry of loss in the back of her mind and looked at the Staryu. She ripped off another part of her dress and tied it around the Staryu's arm. It would leave a scar but she couldn't do anything else for the pokemon. She picked up the pokemon and held it close just like she used to do with her teddy. "Don't worry I'll take care of you. I'll train you so that no one will ever be able to take anyone away from us again." '_Who are you? Why are you not attacking like the ones before?'_ "My name's Emerald. The ones before took away my family as well. But if we work hard enough everyday, one day we can get them back for what they did. What do you think about that?" '_Emerald...I will do whatever it takes. My name is Rasa._'

Emerald stumbled over to a tree just inside of the forest leaving the scene behind her. She sat heavily against the tree still gripping Rasa tight. Rasa was her last anchor to sanity. She could forget about what happened if she was concentrating on making sure that Rasa was okay. "Remember Rasa, one day we will be the best and no one will be able to do this to us again." '_I will never forget, Emerald._'

Green eyes glowed in the darkness as the rain continued to fall. The Starmie had given Emerald a way to communicate with Rasa...but she had also received more...


	2. Chapter 1

Author's Note: Hey guys, I just wanted to say thank you to Yawgmoth for my review because that was my goal for this story . 1 review might not seem like much but since this is my first story I'm happy.

_Disclaimer: I do not in anyway shape or form own pokemon, but I do own Emerald._

Alternate Reality: The Trials of Emerald

Chapter 1

_4 years later..._

A girl with midnight black hair and emerald eyes crouched in the shadows of a building. Her eyes darted left and right before she moved to the next shadow. She heard footsteps and pressed herself against the building. Both eyes narrowed as they passed by without even noticing her presence. That sickly red letter on the front of their uniform made her blood race with rage. When they had passed her position she continued towards her destination, the Pokemon Center.

When the Pokemon Center was in sight she calmly walked out of the shadows and around to the back. She knocked on the backdoor with three hard taps followed by 3 soft taps. The door cracked open a face appeared. "Right on time as usual Emerald." The door opened up enough so that Emerald could slip through.

"Hello Nurse Joy, how are you today?"

"Oh, I'm the same as any other day I suppose." Her eyes looked tired but she smiled at Emerald anyways.

"So how's Rasa doing today, the same healing as usual?"

Emerald's tone got serious, "You know you don't have to heal my pokemon. If anyone ever found out..."

"Oh don't worry about that, I can take care of myself."

Nurse Joy put both of her hands on Emerald's shoulders. "I want to do this. It's the only thing I have to look forward to now. If I get caught the only thing I will regret is not being able to take care of you anymore. I already feel that I don't do enough for you."

"Thank you."

There was a small silence between them before Nurse Joy spoke. "So let me see Rasa so that I can heal her."

Emerald pulled out a pokeball from the folds of her clothes. Nurse joy took the pokeball and walked over to a wall. She ran her hand along it till there was a click and a small passageway appeared. They walked down some stairs into a dimly lit room where there was some equipment that looked like it belonged in a dump. After hooking Rasa up to the second rate machines Nurse Joy and Emerald sat down to talk like they always did.

"So what has been happening in the real world?"

Nurse Joy's mouth became a thin line. "They've finally taken over the Kanto region."

Emerald's eyes widened, "What! But it's only been a week since I've been here. I thought that the Victory Mountain defenses were holding strong."

Emerald watched Nurse Joy's facial expressions carefully; she had never seen her look so...so...defeated. "So did everyone else...but they brought in some secret weapon that decimated everything that went against it. Eventually the Elite Four had to surrender or everyone there would have been slaughtered. There aren't many details but from what I have heard everyone that wasn't killed in the invasion was taken prisoner. No one knows what's happened to them."

Emerald's eyes were downcast. "Even the Elite Four were taken?" Nurse Joy nodded her head sadly.

Emerald stood up with determination in her eyes. "I have to go help them. Rasa and I can free them I know it."

Fear came into Nurse Joy's eyes. "Emerald please listen to reason. Even the Elite Four lost to their power. You only have one pokemon. What can you do that they couldn't?"

Emerald looked away for a moment and her eyes glowed briefly before she turned back around. "I suppose you're right, the best thing I can do now is to train Rasa and myself more."

Emerald saw a relieved look pass across Nurse Joy's face from the corner of her eye. "Emerald, I've never asked before but what kind of training do you put yourself through anyways. I—"

"Don't want me to get hurt, right? I...just try to keep myself in shape, that's all." The machine Rasa was hooked up to started beeping and Nurse Joy walked over to it.

Emerald asked a question that she asked every time she came to get Rasa healed. "Have you managed to find another pokemon for me?"

Nurse Joy handed Emerald the pokeball. "Actually, I have managed to catch one pokemon without them knowing. You'll probably laugh at me though."

Emerald wondered what pokemon it could possibly be, unless it was a...oh... maybe she should be laughing. "Anything that you have would be wonderful." Nurse Joy walked over to a dusty shelf and picked up a pokeball.

"I suppose you are around the age that most used to start their pokemon journeys. I guess it's only right that you receive a pokemon." She handed Emerald the pokeball. Emerald took it and braced herself when she let her new pokemon out. She was right after all. Before her flapping on the ground uselessly was a Magikarp. Honestly she couldn't expect anything more with all the regulations and patrolling that was going on.

She looked at Nurse Joy who had an embarrassed look on her face. "He's wonderful, thank you." Emerald walked over the pathetic pokemon picked him up. He stopped moving immediately. _Hello friend Magikarp, my name is Emerald and I am your new trainer._ If the Magikarp's gaze wasn't perpetually blank she could have sworn that he looked at her. In any case she didn't receive a response.

"So where did you find him?" They started walking up the stairs again.

"I found him in the river; he was stuck in some of the trash that's piled up there."

Emerald looked down at her newest pokemon. "I'm surprised the river hasn't flooded with all of the trash they dump in there." Emerald grabbed her pokeball and a red light engulfed Magikarp. They stopped at the back door.

Nurse Joy enveloped Emerald in a hug. "Be safe." A small smile appeared on Emerald's face. "I will be." Nurse Joy opened the door a crack and looked outside. She motioned to Emerald and Emerald slipped out without a sound. Nurse Joy looked away for a second but when she looked back Emerald was nowhere in sight.

XoXoXoX

Emerald looked back at the town behind her then at the beach in front of her. This was probably the hardest part of her journey into and out of town. There were no shadows to hide in on the beach. Quickly and quietly she sprinted across the sand and slipped into the water. She grabbed Rasa's pokeball and released her. Emerald grabbed onto two of Rasa's arms and whispered to her, "Take us home." They slipped under the waves and disappeared.

XoXoXoX

Emerald stood up on a different beach and dried herself as best she could. She looked over her surroundings; they held both happiness and pain for her. This was the island her family used to live on. To her knowledge no one knew about it except her and the ones the destroyed her life. They had never come back after that night. This was still her home though.

When she was strong enough all those years ago she buried those she could find. It was hard for her and most of the holes were dug right beside the bodies because she wasn't strong enough to move them. The island had all she needed though. Her family had been self-sufficient. There was a well where she could get fresh water from. There were also numerous fruit trees around both planted and native. There also used to be a vegetable patch but she had never really figured out how it worked. She fished for food sometimes for Rasa and herself. All in all it was enough to get by, she couldn't complain.

Emerald lay down on the sand and looked up at the clouds. She did this often to gather her thoughts. The privacy of the island was what she appreciated the most. After her family died everything seemed to happen so fast. By the time she had made it to the town for the first time the takeover of all the regions had begun. It had only been 4 years today that the takeover had begun and now Kanto was defeated. This was a sad day. No one took the takeover serious at first and by the time everyone realized what kind of power they were up against...

She shook her head and muttered to herself, "I don't need to be worrying about all of that." Emerald stood up and beckoned to Rasa. "Come on, it's time to train. Plus we have a new guest today." Emerald took out Magikarp's pokeball and looked at it fondly while walking back to the house. It may be the weakest pokemon out of them all but he was a gift and she would train him nonetheless. Although, how she would do that she still didn't have any idea.

When she arrived at the house she released Magikarp into a fountain that held rainwater. She walked up to it and started talking even though she was fairly sure that its mind was a blank slate. "Hello Magikarp, I'm going to be training with Rasa that Staryu over there. Watch carefully because you're going to be doing this one day." Emerald winked and gave him a small peck on his crown.

Emerald picked up a small pile of pebbles. "Ready Rasa!" She felt the soft touch of Rasa's mind on her own. _Ready Emmy._ Emerald threw the pebbles in rapid succession. A water gun came out and hit every pebble dead on. "Good job! Again!" They did this over and over until Emerald picked up a handful and did something different. "Try this." She threw them all up at once, there must have been a hundred. Rasa didn't miss a beat and quickly stars flew up to meet every pebble and neatly cut them in half. "Good. You know what's next."

Emerald crossed her arms in front of her in an X and shouted, "Give me your best tackle attack!" Rasa came towards her and when Emerald received the tackle her feet skidded on the ground. When she came to a stop she started shaking her arms out. "You're getting pretty good at that." She turned her arms over and saw two bruises forming. She looked up; a spark of challenge had ignited in her eyes. "Again!" Rasa complied and gave another tackle. Every time Emerald would skid further back.

"Hmmm, okay time to move onto the Body Slam."

Emerald took in a deep breath, this was necessary to bring Rasa to her full potential. She looked up and crossed her arms in an X again. "Go." Rasa flew into the air and began to spin faster and faster till she was almost a blur in the air. She came at Emerald just like she did with the tackle.

When Rasa made impact this time though, a horrible cracking sound echoed throughout the island. Both of Emerald's arms had broken from the impact and when her arms had slammed into her body most of her ribs were broken as well. Emerald's eyes glazed over as she let out a small gasp of pain. She fell to her knees her arms dangling uselessly by her side. She began to cough up blood and her eyes were closed tight.

Magikarp jumped out of the fountain and used a pathetic tackle against Staryu. Staryu didn't budge an inch and Magikarp just bounced off and began to uselessly flop on the ground. _Need...help...green-eyed girl..._ This Magikarp was trying to protect Emerald but he had failed. Both pokemon could only watch as Emerald continued to cough up blood.


	3. Chapter 2

_Disclaimer: I do not in anyway shape or form own pokemon, but I do own Emerald._

Alternate Reality: The Trials of Emerald

Chapter 2

Blood dripped from Emerald's mouth and hit the ground. A small smirk formed on her mouth and she let out a chuckle. She opened her eyes and looked at Rasa. Her voice was barely a whisper. "Good one Rasa…guess I forgot the cosmic shield." Emerald's eyes began to glow as she painfully rose to her feet. A white light slowly emanated from her body and the sound of bones resetting echoed throughout the surroundings.

She raised her hand to her mouth and wiped the blood away. Emerald looked down at her hands and clenched them into fists. She squeezed different parts of her forearm and touched her ribs. "See Magi, good as new." She walked over to the flopping Magikarp and picked it up. "Although, I do appreciate the assistance."

Emerald placed Magi in the fountain again. She kneeled so that she was level with him. "I guess I didn't explain the training sessions enough before we started. Rasa and I train like this every moment we can. Today I forgot to use cosmic shield because I was excited to receive you…other days I don't on purpose." Emerald stood up, but her eyes were downcast. "I was…gifted with these powers." She made a fist and held it up in front of her face. Electricity began to cackle and grow around it. She released her fist and the electricity disappeared.

Her eyes narrowed and determination lit up in her eyes. "I won't lie to you Magi. I train for only one reason, revenge. They took my parents and my baby brother away from me. They took your home away from you. They've taken away so much…from everyone."

Emerald looked Magi straight in the eyes trying to find some sign of recognition. "I will ask you to do anything that I can put myself through, but nothing more. I am training myself for the day I can get revenge. When that day comes I want to be ready." She turned to Rasa. "We're going to have to train twice as hard now…the Elite Four was taken. They were some of the most powerful pokemon trainers out there. I'm still not sure how they were beaten..."

There was silence for a few minutes before Emerald smiled. "Let's get to work on that tackle of yours Magi." She crossed her arms in front of her and formed an X. A smirk appeared on her face. "Let's see what you can do."

A rare smile graced Emerald's features. It had been a month since she first received Magi. The progress she had made with him was extraordinary. If there was one thing she could say about her Magikarp, it was that he was determined. She had not expected him to put so much effort into their training sessions before he knew them well. When she first glanced into Magi's eyes she thought that it was empty space, but now she could tell what he was thinking. It just took a different perspective. Staring at them every day for a month was helpful too.

Emerald slowly crawled out of the water and looked around. Everything was clear and she hastily went to the shadows of the many buildings of the city. She was always safe in the shadows. With practiced ease she slipped from shadow to shadow. Sometimes soldiers would pass inches by her and not notice. A little mental persuasion for them not to look at her helped as well.

When she arrived at the last shadow suspicion began to well within her. Her keen eyesight picked up that the door was cracked very slightly. Her instincts told her to turn around and go back to her island. But if something had happened in the pokemon center, Nurse Joy might be in danger. Emerald bit her bottom lip while weighing her choices.

There was always the possibility that Nurse Joy had left it open a crack on accident. But if there was one thing she had learned; it was that one could never be too cautious.

Emerald looked around and made a dash for the back door. When she got there her hand stopped inches away from knocking. If something was wrong she wanted to have the element of surprise. She placed her hand on the door and slowly pushed it open. All of the lights were turned out. That was not a good sign. She quickly scanned the shadows to see if an ambush was waiting for her. When she saw nothing her eyes narrowed. _Odd…_ Shouldn't there have been someone waiting for her? It made sense to catch your opponent off guard.

She entered the building and closed the door behind her. Darkness filled every corner. Her eyes glowed green as she searched for the hidden door and her hand traced the wall until it came to an empty space. Fear began to creep into her heart. The door was already open.

Emerald took a couple deep breaths to calm her nerves. She silently crept down the pitch black stairs. Her eyes stopped glowing before she descended. _I don't want to alert whoever's here; two brightly glowing eyes isn't very good cover. Now if I remember correctly, the light switch is at the bottom of the stairs_. Emerald walked down the stairs silently thanking whoever made them when they didn't squeak. She stared into the the room and turned the lights on. They flickered for a moment before dimly lighting up the room.

Emerald let out a small gasp and all thoughts of scanning the room left her. Her eyes couldn't leave the middle of the room. In the middle of the room was a chair and Nurse Joy was tied to it. Two tears made their way down Emerald's cheeks and her bottom lip began to tremble.

Nurse Joy's head was lolled to the side and her eyes were staring blankly ahead. A red line was on her neck and crimson liquid leaked from it. Emerald was frozen in place; she had always feared this would happen. She had never thought it would actually happen though. If it wasn't for Nurse Joy then she probably wouldn't be alive. Nurse Joy was as important to her as her family was. She was her foster mother almost.

Emerald felt someone come up behind her and cuff her wrists. She was still lost in her own world and didn't struggle. They threw her against the wall and grabbed her face roughly with one hand. Her eyes were still fixed on Nurse Joy. It was only when he spoke that she turned to look at him. There wasn't any emotion on her face or in her eyes.

"What do we have here?" His eyes narrowed. "You're just a kid. I was hoping to find a rouge trainer." He let go of her face and was about to walk away when a glint of red caught his eye. Emerald's secret pocket had been revealed when she was thrown to the ground. He reached and pulled a pokeball from her pocket. An evil smile came to his face as he stared at the pokeball. "This will definitely land me a promotion." He turned to Emerald. "Thanks a lot little girl."

He released Magi and began to laugh as it flopped around on the ground. "I can't believe that woman risked her life to give you a Magikarp. Since this pokemon is probably loyal to you I can't allow it to live." Emerald's mind was still unfocused from the sight of Nurse Joy, but it came into focus when he said that he would kill Magi. "No!" A confident smile appeared on his face. Emerald's eyes narrowed; whatever he was about to say he had said it a lot. "If you want your pokemon to live you could always join—". "Never!" Emerald pulled against her bonds. "You killed my family, why would I ever want to join you."

"If you don't, not only will I kill your pokemon but I'll kill you as well. We don't like to keep prisoners. When I get my promotion you will either be a new recruit or a corpse." He brought out a blood stained knife. Emerald's brain went into overdrive; she needed to get out of this situation. _I can't release Rasa because my hands are bound…I guess I'll need to trust Magi for this one._ "Magi, tackle attack!"

Magi stopped flopping around for a moment and came at the soldier with his most powerful tackle. The man was almost knocked off of his feet and looked at Magi in surprise. "Again!" Magi came at the soldier but he just knocked him away with his arm. "I've changed my mind. I think I'll keep your Magikarp and kill you. I'll get a promotion for turning in this traitorous Nurse Joy anyways." Emerald pulled against her bonds some more, but they were metal and she could not break them. He walked towards her with his knife. "Just a little slit like your friend has over there and it will be over."

Emerald's eyes narrowed. There was no way that she was going to die today from some grunt. Power began to grow within her but then it stopped. A white glow came from behind the soldier and her eyes widened. Something was happening with her Magikarp. The white light began to grow and the grunt turned around in surprise as well. When it disappeared a Gyarados was stooping in the small room.

Gyarados hit the man before he could move and he hit the wall with a loud thud. Before Magi could land a tackle that would have crushed his ribs Emerald yelled for him to stop. She stood up while the man looked warily between her and her Gyarados. Electricity grew around her body and her collected around her wrists. Her cuffs snapped off. "H-how did you do that?" Her eyes glowed green and her voice was calm. "You'll regret killing her and threatening to kill me," she said as if she was talking about the weather.

The grunt huffed. "What's the worst you'll do to me little girl. Kill me? Little girls don't kill people, even freaky ones." He was trying to sound confident but it was easy to see that he was scared. "Stop calling me a little girl." The man flicked his wrist and a dagger came towards her. She raised her hand and it stopped inches away from her palm. She grabbed the dagger from the air and threw it to the side. "You have no idea what I can or will do."

The grunt was backed up against the wall with no weapon and nowhere to go. "If your friend had been more careful this never would have happened." Emerald walked up to him and pinned him to the wall with a wave of her hand. "She was very careful…you're lying."

The man pulled vainly against his invisible bonds. "What are you?" Emerald ignored him. "Why did you kill her? There was no way you could have found out." She applied more pressure. "Because I wanted to…We get whatever we want. I wanted a kiss and she wouldn't give it to me. She tried to run down here, but when she did I found the perfect reason to punish her. This lab is highly illegal. Remember, we don't take prisoners." He chuckled. "But I did get that kiss."

Emerald was silent.

"You wanted the truth didn't you? So what are you going to do now, torture me or get your little pokemon to? As soon as I recover I'll tell everyone who needs to know your description. You won't be able to hide anywhere. Kanto was just the first step. Anyone who has even been seen with you will probably be interrogated then killed as well. But that's if you make it out of the city alive. There are patrols all around the building. If your pokemon does anything it will attract attention. I know you won't do anything except push me against the wall little g—"

"Shut up!" Crimson liquid splattered against her face and silence descended upon the room. Emerald's eyes widened in surprise; slowly she removed her bloodied fist from the middle of the grunt's neck. His lifeless form dropped to the ground. She stared at her hand for a few moments transfixed by the blood dripping off of her fingers. She turned her head towards the large Gyarados that took up half the room.

"…Magi…take me home."

Magi lowered his head and she clumsily got on. With a roar Magi broke through the roof of the pokemon center. Every patrol turned towards the Gyarados. Luckily none of them could get a clear look at the person on his back. They tried to chase after her, but Magi flew as fast as he could towards the island and gently deposited Emerald near the fountain. She washed the blood from her hands and released Rasa.

"What have I done? I-I just got so angry and then…" Tears were falling freely from her eyes.

_You would have had to kill him._

"What?"

_He saw your face…if you are identified you may never get your chance for revenge._

"Shouldn't killing have been part of my revenge Rasa? I had thought about killing all of them when I was training but…I didn't feel better when he was gone."

_Revenge may never make you feel good, but it is the reason you've been training so hard. You started to avenge your family, right?_

"Yes…"

_I did as well. I will only have comfort when everything they are is destroyed. That can only happen one member at a time._

"I didn't know it would be so hard…I thought I had prepared myself for everything."

_We are both still young. Whatever you want to do I will follow you Emmy. If you do not wish to continue I will understand._

"No…"

Emerald's eyes hardened and something in her died. "…I want revenge. If that means I have to kill every single one of them, I will. If I have to kill their pokemon I will. I'll do whatever it takes."

Emerald's head turned toward the city. "They are coming." She turned to her two pokemon and gave them a few quick words. "Magi, I'm very proud of you; you evolved just to protect me. I hope you understand what I had to do. Rasa, thank you for talking with me; you're the only reason I'm still sane." She brought out a pokeball and a red light enveloped Rasa.

Emerald turned towards her Gyarados and he put his head down. She climbed on making sure she had a firm grip and gave her home one last look.

"Take me away from here…away from Kanto…we'll come back when we're ready…"


End file.
